© 2007 Society of Systematic Biologists
Phylogenetic Systematics and Biogeography of Hummingbirds: Bayesian and Maximum Likelihood Analyses of Partitioned Data and Selection of an Appropriate Partitioning Strategy
1 Museum of Vertebrate Zoology, 3101 Valley Life Sciences Building, University of California Berkeley, CA, 94720-3160, USA E-mail: mcguirej{at}berkeley.edu douga{at}ucr.edu najames{at}lsu.edu
2 Museum of Southwestern Biology and Department of Biology, University of New Mexico Albuquerque, NM, 87131-0001, USA
3 Department of Biology, University of California Riverside, 900 University Avenue, Riverside, CA, 92521-0427, USA
4 LSU Museum of Natural Science, 119 Foster Hall, Louisiana State University Baton Rouge, LA, 70803, USA
Edited by Kelly Zamudio, Jack Sullivan
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Abstract |
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Hummingbirds are an important model system in avian biology, but to date the group has been the subject of remarkably few phylogenetic investigations. Here we present partitioned Bayesian and maximum likelihood phylogenetic analyses for 151 of approximately 330 species of hummingbirds and 12 outgroup taxa based on two protein-coding mitochondrial genes (ND2 and ND4), flanking tRNAs, and two nuclear introns (AK1 and BFib). We analyzed these data under several partitioning strategies ranging between unpartitioned and a maximum of nine partitions. In order to select a statistically justified partitioning strategy following partitioned Bayesian analysis, we considered four alternative criteria including Bayes factors, modified versions of the Akaike information criterion for small sample sizes (AICc), Bayesian information criterion (BIC), and a decision-theoretic methodology (DT). Following partitioned maximum likelihood analyses, we selected a best-fitting strategy using hierarchical likelihood ratio tests (hLRTS), the conventional AICc, BIC, and DT, concluding that the most stringent criterion, the performance-based DT, was the most appropriate methodology for selecting amongst partitioning strategies. In the context of our well-resolved and well-supported phylogenetic estimate, we consider the historical biogeography of hummingbirds using ancestral state reconstructions of (1) primary geographic region of occurrence (i.e., South America, Central America, North America, Greater Antilles, Lesser Antilles), (2) Andean or non-Andean geographic distribution, and (3) minimum elevational occurrence. These analyses indicate that the basal hummingbird assemblages originated in the lowlands of South America, that most of the principle clades of hummingbirds (all but Mountain Gems and possibly Bees) originated on this continent, and that there have been many (at least 30) independent invasions of other primary landmasses, especially Central America.
Keywords: Akaike information criterion; ancestral state reconstruction; Bayesian information criterion; Bayes factors; biogeography; branch-length priors; decision theory; hierarchical likelihood-ratio test
Received February 5, 2007; Revised May 18, 2007; Accepted June 19, 2007
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